2-179348942-T-C

Position:

• chr2-179348942-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.477 in 152,154 control chromosomes in the GnomAD database, including 21,036 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (21036 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.723

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72479 AN: 152036 Hom.: 21016 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.511

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.477 AC: 72516 AN: 152154 Hom.: 21036 Cov.: 32 AF XY: 0.487 AC XY: 36192 AN XY: 74380

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.516

Alfa AF: 0.552 Hom.: 5080

Bravo AF: 0.460

Asia WGS AF: 0.631 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.7
DANN	Benign	0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10186547; hg19: chr2-180213669;